Danny Alexander has ended the tax deal set up for the student loan chief executive, Ed Lester (above). Photograph: Slc/PA

At the beginning of May it emerged that more that 2,000 senior public sector officials are being paid 'off the books' through private companies, rather than through the government's payroll, as a way – in some cases – of minimising an individual's tax liability.

It follows earlier revelations about similar practices at the Department of Health and at the very top of the Student Loans Company. I am clear that those holding senior management posts in government departments – and quangos – should not be paid in this way. It is not only unethical, but also unfair for the vast majority of senior public servants who rightly pay the appropriate tax and national insurance contributions.

But despite the lurid headlines, many of these 2,000-plus people are more likely to be specialist consultants working in professions such as IT and HR, rather than senior government managers.

That said, it was deeply disturbing that it appears that 40% of those benefiting from these tax arrangements have been in roles for two years or more – working both under this government and the previous Labour administration. It is clearly wrong and should not have happened.

What the figures reveal is a deep and underlying problem about how we properly reward those tasked with carrying out the current government's programme of reform.

Senior civil servants have chosen a public service career, not primarily for monetary gain but rather to make a difference. It is still essential, however, that their total reward – salary and pension – is at a level that is not only fair and appropriate to the size of job, but also at a level that allows the civil service to continue to attract, motivate and retain the best graduates into the fast stream programme, which is the life blood of the future senior civil service.

Despite this imperative to reward properly, research carried out by Incomes Data Services and published in April found that the approach to pay in the civil service in recent years "has resulted in lower or less evenly distributed basic awards for many civil servants in comparison with the rest of the public sector". It also found that, since 2006, "basic pay settlements have been higher in the private sector than in the public sector".

Added to attacks on public sector pensions – including increased contributions and increased pension age – it is hard to see how the government can justifiably argue that senior public servants are being rewarded appropriately and fairly.

Payments made to consultants through limited companies also exposes another issue: the rather crude working of the recruitment freeze introduced by the government in 2010, which departments have attempted to get around.

Furthermore, it raises the important question of why the government isn't capable of generating good IT people and developing people for senior HR roles? We do need to stand back and look at what roles we need in central government – and the wider public sector – over the next five to 10 years. We should train people and pay them in a way that retains them and doesn't force then to rush into the private sector where the rewards are considerably higher. Failure to take action now will result in a considerable cost to future governments.